Socioeconomic events
The example that would apply to most of us would be racism in the western world.
“In a ‘post-race’ country like America where nothing and no one is racist, where people are more likely to believe in UFO’s than in institutional bias, which does back flips to obfuscate the operations of white hegemonic power and therefore ensure its continuance, anyone seeking to expose white supremacy or battle it is in for some serious uphill. You will be attacked. You will be censured, usually by your own community. People will say that you are obsessed with race and that even mentioning white people in the context of white supremacy is itself racist. These days the average person doesn’t even have to be taught not to bring up white supremacy. Here in our country, as in Mordor, everybody knows not to say the dark lord’s name.” - Junot Diaz
Whites have been the primary driving force in the world for hundreds of years now. Whites are born on top, with significant advantages over other races. Simply put, it's more likely that a minority will be born into a poor uneducated area than a white.
If you're sitting on someone, you wont necessary realize what you're doing, and even if you do, isn't it more comfortable to stay sitting?. If you're being sat on, you will notice.
The bitterness caused by this mechanic, coupled with socioeconomic disadvantages causes minorities to act in a way that is considered inappropriate / uncivilized to western society at greater rates than their wealthy, educated counterparts.
Obviously, whites see a pattern and develop racist thoughts if they haven't learned them from their family and friends already. They stereotype minorities as uneducated and poor because the fact of the matter is that they are in today's world.
Pride
Whites may also inherently see themselves as superior, too. You mentioned that all races have contributed equally to the modern world. Sadly, this is not true. While many races have contributed in huge ways to the ancient world, whites have contributed most to the modern world. A huge amount of technological and philosophical advancement in the modern world can be attributed to whites, regardless of the fact that much of it was built on discoveries by other races.
What this means is that today's whites see a world where the people of africa, india, the middle east, and much of asia is poor both in their native countries and in the US and Europe.
Just as people who watch sports on TV identify with a team, whites identify with their race. They find pride in their race because of its success. This can also lead to thoughts of superiority.
Judging a book by its cover
People like to judge, like to define people by the simplest definition. Stereotyping is a very potent survival tool.
Sure you can assume that only the first lion was a maneater, and that you shouldn't avoid other lions because they might not be - but wouldn't it be easier to just assume that all lions tried to eat humans and avoid them altogether?
Sorry this information is disorganized, just getting my two cents in. I'm sure there are many more reasons, and hey, maybe some of mine are wrong.
Also for context: I'm white, but I have many friends that aren't, friends that I've had discussions with on this topic over a few beers.